[MRG] add picklists to selector protocol and provide initial Index support

[ctb]

This PR adds picklists (#1587) into the selector protocol so that Index.signatures(...) and Index.find(...) both respect picklists, and also introduces it throughout the command-line interface.

In detail, this PR:

• adjusts Index.select(...) to support a picklist keyword argument and adds picklist support to the main Index subclasses;
• adds picklist support to SBT.select(...) and LCA_Database.select(...) as well;
• adds picklist support to load_file_as_signatures(...)
• refactors sourmash sig extract to pass its picklist into load_file_as_signatures(...), rather than do ad hoc picklisting;
• adds --picklist support to compare, gather, index, lca index, prefetch, and search

Note, I decided against adding picklists to lca summarize and lca classify for now, since I think we may be end-of-life-ing LCA databases soon.

This does not implement any optimizations for picklist-intersected database searches yet, but they are coming - see #1590!

TODO:

• add docs
• verify that prefetch CSV can be used as a picklist
• verify that 'index' with picklist == 'index' then 'search' with picklist

[codecov]

Codecov Report

Merging #1588 (8e5fb8d) into add/picklist (14b87d4) will decrease coverage by 0.17%.
The diff coverage is 66.66%.

@@               Coverage Diff                @@
##           add/picklist    #1588      +/-   ##
================================================
- Coverage         89.34%   89.16%   -0.18%     
================================================
  Files                76       76              
  Lines              6717     6739      +22     
  Branches           1198     1207       +9     
================================================
+ Hits               6001     6009       +8     
- Misses              507      514       +7     
- Partials            209      216       +7     

Flag	Coverage Δ
python	89.16% <66.66%> (-0.18%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/sourmash/sig/picklist.py	87.17% <40.00%> (-7.35%)	⬇️
src/sourmash/lca/lca_db.py	90.21% <60.00%> (-1.01%)	⬇️
src/sourmash/sbt.py	80.75% <63.63%> (-0.30%)	⬇️
src/sourmash/index.py	99.03% <100.00%> (+<0.01%)	⬆️
src/sourmash/sig/__main__.py	91.64% <100.00%> (-0.04%)	⬇️
src/sourmash/sourmash_args.py	93.71% <100.00%> (ø)

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[codecov-commenter]

Codecov Report

Merging #1588 (565428b) into latest (a2d438d) will increase coverage by 0.10%.
The diff coverage is 99.11%.

@@            Coverage Diff             @@
##           latest    #1588      +/-   ##
==========================================
+ Coverage   81.19%   81.29%   +0.10%     
==========================================
  Files         103      103              
  Lines       10423    10485      +62     
  Branches     1198     1217      +19     
==========================================
+ Hits         8463     8524      +61     
- Misses       1751     1753       +2     
+ Partials      209      208       -1     

Flag	Coverage Δ
python	89.42% <99.11%> (+0.08%)	⬆️
rust	66.43% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/sourmash/commands.py	86.46% <95.23%> (+0.21%)	⬆️
src/sourmash/cli/compare.py	100.00% <100.00%> (ø)
src/sourmash/cli/gather.py	100.00% <100.00%> (ø)
src/sourmash/cli/index.py	100.00% <100.00%> (ø)
src/sourmash/cli/lca/index.py	100.00% <100.00%> (ø)
src/sourmash/cli/prefetch.py	100.00% <100.00%> (ø)
src/sourmash/cli/search.py	100.00% <100.00%> (ø)
src/sourmash/cli/sig/extract.py	100.00% <100.00%> (ø)
src/sourmash/cli/utils.py	100.00% <100.00%> (ø)
src/sourmash/index.py	99.03% <100.00%> (+<0.01%)	⬆️
... and 7 more

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[ctb]

Ready for review @bluegenes. There's a few minor issues to do with our test infrastructure that I'll deal with before considering merge, but the PR is feature complete ;)

[ctb]

ok, tests are actually passing now, too! Ready for review and maybe merge!

[bluegenes]

lgtm! looking forward to actually playing around with picklists soon :)

[ctb]

thank you!!